utility.cpp File Reference

#include <algorithm>
#include <cmath>
#include <limits>
#include <string>
#include <sstream>
#include <fstream>
#include <iostream>
#include <iomanip>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include "copasi/copasi.h"
#include "utility.h"
#include "CCopasiMessage.h"

Macros
#define	toBeEscaped   "\\\""

Functions
bool	containsTag (const std::string &filename, const std::string &tagname, int numLines)
void	FixSName (const std::string &original, std::string &fixed)
bool	isNumber (const std::string &str)
std::string	ISODateTime (tm *pTime)
bool	isProbablySBML (const std::string &filename)
std::string	LocalTimeStamp ()
std::string	nameToSbmlId (const std::string &name)
std::string	pointerToString (const void *pVoid)
std::string	quote (const std::string &name, const std::string &additionalEscapes)
std::string	StringPrint (const char *format,...)
bool	stringReplace (std::string &str, const std::string &target, const std::string &replacement)
void *	stringToPointer (const std::string str)
double	strToDouble (const char *str, char const **pTail)
bool	strToIndex (const std::string &str, size_t &index)
C_INT32	strToInt (const char *str, char const **pTail)
unsigned C_INT32	strToUnsignedInt (const char *str, char const **pTail)
time_t	timeFromUTC (const std::string utc)
std::string	unQuote (const std::string &name)
std::string	UTCTimeStamp ()
size_t	utf8Length (const std::string &str)

Macro Definition Documentation

toBeEscaped

#define toBeEscaped   "\\\""

Function Documentation

containsTag()

bool containsTag	(	const std::string &	filename,
		const std::string &	tagname,
		int	numLines = 10
	)

Test whether a given XML tag is present in the first number of lines of a given file.

Parameters

filename	the filename to be tested
tagname	the tag name to be tested for
numLines	the number of lines to be tested (default 10)

Returns

boolean indicating whether the tag appeared in the first numLines.

Referenced by isProbablySBML().

FixSName()

void FixSName	(	const std::string &	original,
		std::string &	fixed
	)

isNumber()

bool isNumber

(

const std::string &

str

)

Check whether the given string represents a number

Parameters

const

std::string & str

Returns

bool isNumber

References strToDouble().

Referenced by COptItem::compileLowerBound(), COptItem::compileUpperBound(), ConverterASTNode::ConverterASTNode(), CMetabNameInterface::createUniqueDisplayName(), CMetabNameInterface::getDisplayName(), COptItem::setLowerBound(), CDataObject::setObjectName(), COptItem::setUpperBound(), and CChemEqInterface::writeElement().

ISODateTime()

std::string ISODateTime

(

tm *

pTime

)

Returns the time pointed to by pTime in ISO format

Referenced by COptLogItem::fillString(), LocalTimeStamp(), and UTCTimeStamp().

isProbablySBML()

bool isProbablySBML

(

const std::string &

filename

)

Tests whether the file is SBML by reading the first 10 lines and looking for the presence of the sbml tag.

Parameters

filename

the filename to be tested

Returns

true, if the first 10 lines contain the sbml tag, false otherwise.

References containsTag().

Referenced by CDataModel::addModel().

LocalTimeStamp()

std::string LocalTimeStamp

(

)

Returns the current local time in ISO format

References ISODateTime().

Referenced by COptLogEntry::COptLogEntry(), and CCopasiMessage::handler().

nameToSbmlId()

std::string nameToSbmlId

(

const std::string &

name

)

Convert a utf8 encoded name to a XmlId

Parameters

const

std::string & name

Returns

std::string SbmlId

Referenced by CSBMLExporter::createFunctionDefinition(), and CSBMLExporter::createUniqueId().

pointerToString()

std::string pointerToString

(

const void *

pVoid

)

Convert a void pointer to a string

Parameters

const

void * pVoid

Returns

std::string str

References fatalError.

Referenced by CEvaluationNodeObject::CEvaluationNodeObject(), CMathEvent::CAssignment::compile(), CMathObject::compileDependentMass(), CMathObject::compileFlux(), CMathObject::compileParticleFlux(), CMathObject::compilePropensity(), CMathObject::compileReactionNoise(), CMathObject::compileTotalMass(), CMathObject::compileTransitionTime(), CMathObject::createExtensiveNoiseExpression(), CMathObject::createExtensiveODERateExpression(), CMathObject::createExtensiveReactionNoiseExpression(), CMathObject::createExtensiveReactionRateExpression(), CMathObject::createExtensiveValueExpression(), CMathObject::createIntensiveRateExpression(), CMathObject::createIntensiveValueExpression(), CMathDelay::modifyMathObject(), and CEvaluationNodeObject::setObjectValuePtr().

quote()

std::string quote	(	const std::string &	name,
		const std::string &	additionalEscapes = ""
	)

Surround a name with quotes if the name contains a space or double quote else the name is returned unmodified. In the quoted name " and \ are escaped. The parameter additionalEscapes forces quotes around names containing any of the character in the parameter.

Parameters

const	std::string & name
const	std::string & additionalEscapes (default: "")

Returns

std::string quote

References toBeEscaped.

Referenced by CChemEqInterface::addModifier(), CMetabNameInterface::createUniqueDisplayName(), CEvaluationNodeCall::getBerkeleyMadonnaString(), CEvaluationNodeCall::getCCodeString(), CEvaluationNodeCall::getData(), CMetabNameInterface::getDisplayName(), CEvaluationNodeCall::getDisplayString(), CEvaluationNodeCall::getInfix(), CEvaluationNodeCall::getMMLString(), CEvaluationNodeCall::getXPPString(), CUnitDefinitionDB::quoteSymbol(), CEvaluationNodeCall::setData(), and CMetabNameInterface::splitDisplayName().

StringPrint()

std::string StringPrint	(	const char *	format,
			...
	)

sprintf like function for strings

Parameters

const char *	format sprintf like format string
...

Returns

"string"

References C_INT32, and INITIALTEXTSIZE.

Referenced by CDataArray::addElementReference(), CExperimentSet::addExperiment(), CExperiment::elevateChildren(), CDataArray::getAnnotationsString(), CExperimentObjectMap::getDefaultScale(), CExperimentObjectMap::getName(), CExperimentObjectMap::getObjectCN(), CExperimentObjectMap::getRole(), CExperimentObjectMap::getScale(), CCopasiTimeVariable::LL2String(), CReaction::loadOld(), CReaction::loadOneRole(), ParameterDescriptionHandler::processStart(), CExperimentObjectMap::setNumCols(), CExperimentObjectMap::setObjectCN(), CExperimentObjectMap::setRole(), CExperimentObjectMap::setScale(), and CVersion::setString().

stringReplace()

bool stringReplace	(	std::string &	str,
		const std::string &	target,
		const std::string &	replacement
	)

Replaces the all occurrences of target string in str with the replacement and returns true if the target string was replaced

Parameters

std::string	& str
const	std::string & target
const	std::string & replacement

Returns

bool replaced

Referenced by CUnit::buildExpression(), and CModel::replaceInExpressions().

stringToPointer()

void* stringToPointer

(

const std::string

str

)

Convert a character sequence to a void pointer

Parameters

const

std::string str

Returns

void * pVoid

Referenced by CEvaluationNodeObject::CEvaluationNodeObject(), CEvaluationNodeObject::compile(), and CMathExpression::relocate().

strToDouble()

double strToDouble	(	const char *	str,
		char const **	pTail = NULL
	)

Convert a character sequence to a double

Parameters

const	char * str
char	const ** pTail (default: NULL)

Returns

double

Referenced by CEvaluationNodeNumber::CEvaluationNodeNumber(), COptItem::compileLowerBound(), COptItem::compileUpperBound(), CReadConfig::getVariable(), isNumber(), EllipseHandler::processStart(), GroupHandler::processStart(), PolygonHandler::processStart(), RectangleHandler::processStart(), RenderCurveHandler::processStart(), RenderTextHandler::processStart(), COptItem::setLowerBound(), COptItem::setUpperBound(), and CEvaluationNodeNumber::toAST().

strToIndex()

bool strToIndex	(	const std::string &	str,
		size_t &	index
	)

Convert a string to a size_t index. Returns true if the conversion is successful, i.e., the whole string has been converted.

Parameters

const	std::string & str
size_t	& index

Returns

bool success

References C_INVALID_INDEX.

Referenced by CDataArray::cnToIndex(), CDataArray::displayNamesToCN(), CCommonName::getElementIndex(), and CArrayElementReference::updateObjectName().

strToInt()

C_INT32 strToInt	(	const char *	str,
		char const **	pTail = NULL
	)

Convert a character sequence to a double

Parameters

const	char * str
char	const ** pTail (default: NULL)

Returns

C_INT32

References C_INT32.

Referenced by COPASIHandler::processStart(), ParameterHandler::processStart(), and CVersion::setVersion().

strToUnsignedInt()

unsigned C_INT32 strToUnsignedInt	(	const char *	str,
		char const **	pTail = NULL
	)

Convert a character sequence to a double

Parameters

const	char * str
char	const ** pTail (default: NULL)

Returns

unsigned C_INT32

References C_INT32.

Referenced by CCopasiParameterGroup::getObject(), CompartmentHandler::processStart(), ParameterDescriptionHandler::processStart(), ParameterHandler::processStart(), ReportDefinitionHandler::processStart(), and SliderHandler::processStart().

timeFromUTC()

time_t timeFromUTC

(

const std::string

utc

)

Converts the UTC time to time_t

Parameters

const

std::string utc

Returns

time_t time

Referenced by CCheckForUpdates::checkRequired().

unQuote()

std::string unQuote

(

const std::string &

name

)

Unesacape a quoted name. If the name is surrounded by quotes these are removed and included escape sequences '.' are reduced to '.' else the name is returned unmodified.

Parameters

const

std::string & name

Returns

std::string unQuote

Referenced by CModel::findMetabByName(), CEvaluationNodeCall::getData(), CDataVectorN< CType >::getIndex(), CUnitDefinitionDB::getUnitDefFromSymbol(), and CEvaluationNodeCall::setData().

UTCTimeStamp()

std::string UTCTimeStamp

(

)

Returns the current time in ISO format

References ISODateTime().

Referenced by CMIRIAMInfo::addDefaultCreatedDT(), CModelVersionHierarchy::addVersion(), CCheckForUpdates::checkRequired(), CFitProblem::createParameterSet(), CCopasiTimer::print(), CConfigurationFile::CXML::save(), CCopasiXML::save(), CCopasiXML::saveModelParameterSets(), and CCheckForUpdates::setChecked().

utf8Length()

size_t utf8Length

(

const std::string &

str

)

calculate the number of utf8 characters in a givent string

Parameters

const

std::string & str

Returns

size_t utf8Length

Referenced by SBMLUnitSupport::createUnitExpressionFor().